Biology subjects

Dudragne, L.

Publications and source records attributed to Dudragne, L..

4 recordsLinked to original sources

bioRxiv2025

Diversity and distribution of the subtelomeric Y' elements across Saccharomyces cerevisiae

The subtelomeric regions of eukaryotic chromosomes harbor repeated elements that contribute to genomic plasticity and adaptation. In Saccharomyces cerevisiae, the Y elements represent a major class of subtelomeric repeats, yet their diversity and evolutionary dynamics remain incompletely characterized. Here, we analyzed Y elements across 54 S. cerevisiae strains using high-quality telomere-to-telomere genome assemblies. We detected 893 high-confidence Y elements, which we classified into 12 major clusters, revealing a broader structural diversity than previously described, including canonical short ([~]5.2 kb) and long ([~]6.7 kb) elements, intermediate-size classes (mid1 and mid2), and a novel family containing CA-rich repeats. Sequence analyses showed that open reading frames (ORFs), including those encoding the putative Y-Help1 helicase, are highly conserved within clusters, suggesting selective maintenance of functional sequences. The distribution of Y elements varied widely across strains and chromosome extremities, with some strains lacking Y entirely and others, such as the clinical ADI isolate, carrying up to 149 copies. Interstitial telomeric sequences (ITS) were variably associated with Y elements and tandem Y repeats, potentially facilitating recombination and amplification. Analysis of telomere length data further revealed that the presence of long Y' elements, but not Y elements from other clusters, at the subtelomere is correlated with shorter telomeres at the same chromosome end. Our results provide the most comprehensive catalog of S. cerevisiae Y elements to date, uncovering unexpected structural and sequence diversity, and a potentially functional role in telomere length regulation.

genomics↗

bioRxiv2025

Transient telomere uncapping triggers telomeric and subtelomeric rearrangements

Telomeres are nucleoprotein structures that cap the extremities of eukaryotic linear chromosomes, thus preventing them from being detected as DNA damage. Telomere uncapping poses a profound threat to genome integrity, yet the immediate consequences of transient uncapping remain unclear. In Saccharomyces cerevisiae, the Cdc13-Stn1-Ten1 complex caps telomeres and limits resection, which would otherwise lead to DNA damage checkpoint activation. Here, using the temperature-sensitive cdc13-1 allele, we demonstrate that even transient telomere uncapping induces extensive genomic rearrangements within a few cell cycles, despite a functional DNA damage checkpoint. Two distinct rearrangement signatures were observed in cells surviving transient uncapping: one characterized by the reorganization and recombination of the subtelomeric region, mostly involving the Y elements, and the other exhibiting massively elongated telomeres up to 10 kb, corresponding to a [~]30-fold increase. Long-read sequencing revealed that the genomic instability was confined to the subtelomere and telomere regions, and evidenced Y' element loss/amplification, terminal duplication of chromosome ends, and telomeric-circle-driven amplification of telomere repeats. Rearrangements unfold over multiple generations and require the homologous recombination factor Rad52 and the Pol{delta} subunit Pol32, which is essential for break-induced replication. The recombination proteins Rad51 and Rad59 also contribute to the rearrangements in partially independent pathways. Remarkably, survivors with elongated telomeres demonstrate robust resistance to subsequent telomere uncapping, in a Rad52-dependent manner. Our findings provide novel insights into the consequences of transient telomere uncapping for genome stability, a process that might contribute to subtelomere and telomere dynamics and evolution.

molecular biology↗

bioRxiv2025

The CST complex mediates a post-resection non-homologous end-joining repair pathway and promotes local deletions

Repair of a DNA double-strand break (DSB) by non-homologous end-joining (NHEJ) generally leaves an intact or minimally modified DNA sequence. Resection initiation exposes single-stranded DNA and directs repair towards homology-dependent pathways and away from NHEJ. Therefore, NHEJ is not thought to be an available repair pathway once the DSB is resected. Here, we report that the Cdc13/Stn1/Ten1 (CST) complex, well characterized for its telomere-associated functions, acts after resection initiation to mediate a backup NHEJ repair. We found a CST-specific mutation signature after DSB repair, characterized by deletions of 5-85 bp, mostly dependent on NHEJ. In contrast, NHEJ-mediated small deletions of 1-4 bp and insertions are not affected in CST mutants. The interaction between CST and Pol-primase is critical for these intermediate size deletions, suggesting a role for fill-in synthesis. Consistently, in stn1{Delta} and Pol-primase mutant deficient for interaction with CST, resection is increased, leading to larger deletions of several kilobases mediated by microhomologies. Collectively, these results depict a more complex picture of repair pathway choice where CST allows a post-resection NHEJ repair, promoting local deletions but guarding against much larger and potentially more deleterious deletions and rearrangements.

molecular biology↗

bioRxiv2021

A comprehensive series of temporal transcription factors in the fly visual system

The brain consists of thousands of different neuronal types that are generated through multiple divisions of neuronal stem cells. These stem cells have the capacity to generate different neuronal types at different stages of their development. In Drosophila, this temporal patterning is driven by the successive expression of temporal transcription factors (tTFs). While a number of tTFs are known in different animals and across various parts of the nervous system, these have been mostly identified by informed guesses and antibody availability. We used single-cell mRNA sequencing to identify the complete series of tTFs that specify most Drosophila medulla neurons in the optic lobe. We tested the genetic interactions among these tTFs. While we verify the general principle that tTFs regulate the progression of the series by activating the next tTFs in the series and repressing the previous ones, we also identify more complex regulations. Two of the tTFs, Eyeless and Dichaete, act as hubs integrating the input of several upstream tTFs before allowing the series to progress and in turn regulating the expression of several downstream tTFs. Moreover, we show that tTFs not only specify neuronal identity by controlling the expression of cell type-specific genes. Finally, we describe the very first steps of neuronal differentiation and find that terminal differentiation genes, such as neurotransmitter-related genes, are present as transcripts, but not as proteins, in immature larval neurons days before they are being used in functioning neurons; we show that these mechanisms are conserved in humans. Our results offer a comprehensive description of a temporal series of tTFs in a neuronal system, offering mechanistic insights into the regulation of the progression of the series and the regulation of neuronal diversity. This represents a proof-of-principle for the use of single-cell mRNA sequencing for the comparison of temporal patterning across phyla that can lead to an understanding of how the human brain develops and how it has evolved.

developmental biology↗